Technical Abstract:
We are building high-resolution radiation hybrid maps of all 29 bovine autosomes and chromosome X, using a 58,000-marker genotyping assay, and a 12,000-rad whole-genome radiation hybrid (RH) panel. To accommodate the large number of markers, and to automate the map building procedure, a software pipeline was constructed to process the data in the following manner. First, a custom program is used to parse the output from the Illumina genotyping system, to determine which markers are present in each RH cell line. In parallel to this procedure, each marker is located on the current bovine and human genome assemblies using BLAST. The marker positions on the bovine assembly and the marker calls are then analyzed using CarthaGene’s comparative mapping algorithm, which uses both sets of information to determine marker order. Lastly, maps are visualized and compared to the bovine and human genome assemblies using AutoGRAPH. The entire process runs in a distributed fashion on a 30-node computing cluster, allowing maps to be rebuilt relatively quickly using alternative parameters or reference assemblies. This pipeline should be applicable to other species for which similar RH panel and genotyping resources are available. The maps generated using this approach should aid in the assembly of problematic genome regions, and in turn facilitate haplotype construction and candidate gene searches.